65 research outputs found
From aggressive driving to molecular motor traffic
Motivated by recent experimental results for the step sizes of dynein motor
proteins, we develope a cellular automata model for intra-cellular traffic of
dynein motors incorporating special features of the hindrance-dependent step
size of the individual motors. We begin by investigating the properties of the
aggressive driving model (ADM), a simple cellular automata-based model of
vehicular traffic, a unique feature of which is that it allows a natural
extension to capture the essential features of dynein motor traffic. We first
calculate several collective properties of the ADM, under both periodic and
open boundary conditions, analytically using two different mean-field
approaches as well as by carrying out computer simulations. Then we extend the
ADM by incorporating the possibilities of attachment and detachment of motors
on the track which is a common feature of a large class of motor proteins that
are collectively referred to as cytoskeletal motors. The interplay of the
boundary and bulk dynamics of attachment and detachment of the motors to the
track gives rise a phase where high and low density phases separated by a
stable domain wall coexist. We also compare and contrast our results with the
model of Parmeggiani et. al. (Phys. Rev. Lett. {\bf 90}, 086601 (2003)) which
can be regarded as a minimal model for traffic of a closely related family of
motor proteins called kinesin. Finally, we compare the transportation
efficiencies of dynein and kinesin motors over a range of values of the model
parameters.Comment: Final Version Accepted for Publication in J. Phys. A (IOP, UK
Evolution of Spatially Inhomogeneous Eco-Systems: An Unified Model Based Approach
Recently we have extended our the "unified" model of evolutionary ecology to
incorporate the {\it spatial inhomogeneities} of the eco-system and the {\it
migration} of individual organisms from one patch to another within the same
eco-system. In this paper an extension of our recent model is investigated so
as to describe the {\it migration} and {\it speciation} in a more realistic
way.Comment: Latex, 10 pages, 8 figure
Dynamic instability of microtubules: effect of catastrophe-suppressing drugs
Microtubules are stiff filamentary proteins that constitute an important
component of the cytoskeleton of cells. These are known to exhibit a dynamic
instability. A steadily growing microtubule can suddenly start depolymerizing
very rapidly; this phenomenon is known as ``catastrophe''. However, often a
shrinking microtubule is ``rescued'' and starts polymerizing again. Here we
develope a model for the polymerization-depolymerization dynamics of
microtubules in the presence of {\it catastrophe-suppressing drugs}. Solving
the dynamical equations in the steady-state, we derive exact analytical
expressions for the length distributions of the microtubules tipped with
drug-bound tubulin subunits as well as those of the microtubules, in the
growing and shrinking phases, tipped with drug-free pure tubulin subunits. We
also examine the stability of the steady-state solutions.Comment: Minor corrections; final published versio
Competition of coarsening and shredding of clusters in a driven diffusive lattice gas
We investigate a driven diffusive lattice gas model with two oppositely
moving species of particles. The model is motivated by bi-directional traffic
of ants on a pre-existing trail. A third species, corresponding to pheromones
used by the ants for communication, is not conserved and mediates interactions
between the particles. Here we study the spatio-temporal organization of the
particles. In the uni-directional variant of this model it is known to be
determined by the formation and coarsening of ``loose clusters''. For our
bi-directional model, we show that the interaction of oppositely moving
clusters is essential. In the late stages of evolution the cluster size
oscillates because of a competition between their `shredding' during encounters
with oppositely moving counterparts and subsequent "coarsening" during
collision-free evolution. We also establish a nontrivial dependence of the
spatio-temporal organization on the system size
Evolutionary ecology in-silico:evolving foodwebs, migrating population and speciation
We have generalized our ``unified'' model of evolutionary ecology by taking
into account the possible movements of the organisms from one ``patch'' to
another within the same eco-system. We model the spatial extension of the
eco-system (i.e., the geography) by a square lattice where each site
corresponds to a distinct ``patch''. A self-organizing hierarchical food web
describes the prey-predator relations in the eco-system. The same species at
different patches have identical food habits but differ from each other in
their reproductive characteristic features. By carrying out computer
simulations up to time steps, we found that, depending on the values of
the set of parameters, the distribution of the lifetimes of the species can be
either exponential or a combination of power laws. Some of the other features
of our ``unified'' model turn out to be robust against migration of the
organisms.Comment: 12 pages of PS file, including LATEX text and 9 EPS figure
Using Computational modeling to understand in-vitro and in-vivo transport by molecular motors
by Ambarish Kunwa
Alpine snowpit profiles of polar organic compounds from Mt. Tateyama central Japan: Atmospheric transport of organic pollutants with Asian dust
Snowpit samples (n = 10) were collected (19 April 2008) from the snowpit sequences (depth 6.60 m) at the Murodo-Daira site (36.58 degrees N, 137.60 degrees E, elevation of 2450 m a.s.l.) of Mt. Tateyama (3015 m a.s.l.), central Japan. The first time, low molecular weight diacids, omega-oxoacids, pyruvic acid, and alpha-dicarbonyls were measured for this snowpit sequence. Higher concentrations of short-chain diacids (C-2-C-5) are observed in dusty snow than nondusty snow samples. Longer chain diacids (C-7-C-12) are significant in granular and dusty snow samples. Aromatic and aliphatic unsaturated diacids showed higher concentrations in the slightly dusty layer deposited in winter. Except for a clean layer, molecular distributions of diacids are characterized by the predominance of oxalic acid (C-2, ave, 20 +/- 22 ng/g-snow) followed by succinic (C-4, 7.2 +/- 5.9 ng/g-snow), and malonic acids (C-3, 3.3 +/- 2.9 ng/g-snow) for all the snow layers. Lower C-3/C-4 ratios (0.46) suggest that organic aerosols are rather fresh without serious photochemical aging during the long-range transport over central Japan. The higher concentrations of the secondary species in dusty snow than non-dusty samples were mainly attributed to the heterogeneous reaction. The strong correlations of incloud oxidation products of isoprene, aromatic acids, and fatty acids suggest that condensation, oxidation, and photolysis are important reaction mechanisms for the formation of diacids. Chinese Loess (Kosa particles) and Mongolian Gobi desert's dust provided the surface area for polar organic compounds, traveled to several thousand kilometers in the lower troposphere, and snow metamorphism altered the chemical composition of diacids and related compounds
Unification of small and large time scales for biological evolution: deviations from power law
We develop a unified model that describes both "micro" and "macro" evolutions within a single theoretical framework. The ecosystem is described as a dynamic network; the population dynamics at each node of this network describes the "microevolution" over ecological time scales (i.e., birth, ageing, and natural death of individual organisms), while the appearance of new nodes, the slow changes of the links, and the disappearance of existing nodes accounts for the "macroevolution" over geological time scales (i.e., the origination, evolution, and extinction of species). In contrast to several earlier claims in the literature, we observe strong deviations from power law in the regime of long lifetimes
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